FMO DATABASE

FMODB ID: 6YYZZ

Calculation Name: 4KK4-A-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 4KK4

Chain ID: A

ChEMBL ID:

UniProt ID: P39155

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	152
LigandCharge	SEP=-2
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1505234.590828
FMO2-HF: Nuclear repulsion	1444928.981465
FMO2-HF: Total energy	-60305.609364
FMO2-MP2: Total energy	-60480.608721

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-24.992	-27.607	34.793	-15.634	-16.542	-0.119

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.084 / q_NPA : -0.052

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	ILE	0	-0.002	-0.006	3.503	1.482	3.184	0.025	-0.477	-1.250	0.003
4	A	4	ILE	0	0.005	0.003	6.100	-0.454	-0.454	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.013	-0.005	9.835	0.151	0.151	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.025	0.002	12.674	-0.113	-0.113	0.000	0.000	0.000	0.000
7	A	7	SEP	-2	-1.532	-1.705	15.923	0.389	0.389	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.033	0.008	19.548	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.032	0.006	22.891	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.011	-0.030	16.647	-0.056	-0.056	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.017	-0.002	20.249	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.035	-0.014	22.161	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.863	0.903	19.455	-0.204	-0.204	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.010	0.007	15.980	0.025	0.025	0.000	0.000	0.000	0.000
15	A	15	PRO	0	0.032	0.029	15.677	0.041	0.041	0.000	0.000	0.000	0.000
16	A	16	MET	0	-0.012	-0.004	17.097	0.014	0.014	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.011	0.003	13.944	0.025	0.025	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.787	-0.888	11.813	0.251	0.251	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.023	-0.014	12.858	0.041	0.041	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.019	-0.016	15.278	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.029	-0.005	6.352	0.011	0.011	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.903	0.960	10.679	-0.187	-0.187	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.024	0.002	11.714	0.015	0.015	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.028	-0.027	12.189	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.019	-0.005	8.344	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.888	-0.933	10.362	0.490	0.490	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.822	0.921	12.041	-0.377	-0.377	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-1.002	-1.011	11.683	0.609	0.609	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.007	0.018	10.962	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.083	-0.047	6.379	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.034	-0.015	3.654	-0.798	0.172	0.223	-0.356	-0.837	-0.002
32	A	32	VAL	0	-0.005	-0.006	2.382	-3.702	-1.089	2.622	-1.915	-3.320	-0.018
33	A	33	ASN	0	-0.053	-0.033	2.950	-1.107	0.315	0.378	-0.332	-1.468	0.002
34	A	34	VAL	0	-0.041	-0.020	4.664	-0.538	-0.597	0.000	-0.022	0.081	0.000
35	A	35	ARG	1	0.868	0.900	6.198	0.820	0.820	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.031	-0.027	9.976	0.136	0.136	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.024	0.017	13.403	-0.076	-0.076	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.041	-0.010	15.839	0.058	0.058	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.013	-0.024	19.304	-0.030	-0.030	0.000	0.000	0.000	0.000
40	A	40	PHE	0	-0.058	-0.028	21.050	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.020	0.023	20.810	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.023	-0.019	22.844	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.017	0.006	20.933	0.010	0.010	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.092	-0.036	22.331	0.010	0.010	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.042	0.029	23.504	0.005	0.005	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.996	1.012	22.416	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.051	0.027	21.679	0.005	0.005	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.008	-0.013	23.474	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.026	-0.004	26.567	0.009	0.009	0.000	0.000	0.000	0.000
50	A	50	HIS	0	-0.003	0.004	28.698	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.043	0.033	23.117	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.038	-0.025	24.051	0.014	0.014	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.892	-0.946	25.379	0.117	0.117	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.018	0.000	24.862	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.003	-0.002	19.265	0.014	0.014	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.003	0.019	23.270	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.926	-0.966	25.921	0.129	0.129	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.830	0.920	22.662	-0.217	-0.217	0.000	0.000	0.000	0.000
59	A	59	HIS	0	-0.041	-0.020	23.115	0.009	0.009	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.006	0.008	18.094	0.012	0.012	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.001	-0.004	21.203	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.017	-0.003	18.972	0.007	0.007	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.056	-0.036	19.622	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.005	-0.001	16.291	0.006	0.006	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.022	-0.007	18.044	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.035	-0.020	17.984	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.015	-0.022	16.140	-0.040	-0.040	0.000	0.000	0.000	0.000
68	A	68	PRO	0	-0.007	0.005	18.048	0.032	0.032	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.026	0.010	13.861	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.017	0.007	14.729	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.857	-0.958	14.862	-0.171	-0.171	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.946	-0.973	12.883	-0.448	-0.448	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.044	-0.021	10.064	-0.137	-0.137	0.000	0.000	0.000	0.000
74	A	74	MET	0	-0.027	-0.008	10.046	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.990	-0.988	10.475	-0.910	-0.910	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.005	0.008	6.416	-0.086	-0.086	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.000	0.021	5.943	-0.770	-0.770	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.780	-0.875	1.644	-11.338	-25.360	29.791	-10.466	-5.302	-0.089
79	A	79	LEU	0	-0.096	-0.048	4.439	0.091	0.263	-0.001	-0.025	-0.146	0.000
80	A	80	VAL	0	0.005	-0.001	6.840	-0.391	-0.391	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.004	-0.001	9.203	-0.049	-0.049	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.003	-0.006	12.384	-0.106	-0.106	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.013	-0.002	15.682	0.032	0.032	0.000	0.000	0.000	0.000
84	A	84	THR	0	0.002	0.003	18.516	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	85	HIS	0	0.059	0.001	20.341	0.019	0.019	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.007	-0.001	22.071	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	87	HIS	0	-0.009	-0.005	19.218	0.009	0.009	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.891	0.943	17.032	-0.413	-0.413	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.030	-0.024	18.966	0.007	0.007	0.000	0.000	0.000	0.000
90	A	90	ILE	0	0.000	0.007	21.747	-0.024	-0.024	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.051	0.022	15.338	-0.027	-0.027	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.035	-0.021	18.565	-0.033	-0.033	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.112	-0.054	19.431	-0.029	-0.029	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.015	-0.005	20.594	-0.025	-0.025	0.000	0.000	0.000	0.000
95	A	95	PHE	0	0.043	0.023	16.421	-0.025	-0.025	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.031	0.014	17.002	0.015	0.015	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.908	0.950	16.024	0.258	0.258	0.000	0.000	0.000	0.000
98	A	98	TYR	0	0.015	-0.001	12.175	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.956	0.976	13.218	-0.031	-0.031	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.938	-0.958	13.271	0.238	0.238	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.827	0.929	8.131	0.369	0.369	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.035	-0.010	10.432	0.199	0.199	0.000	0.000	0.000	0.000
103	A	103	PHE	0	-0.006	0.000	11.428	-0.071	-0.071	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.012	-0.011	14.372	0.035	0.035	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.043	0.017	12.698	0.073	0.073	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.864	0.915	14.914	-0.282	-0.282	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.779	-0.829	16.630	0.460	0.460	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.009	-0.008	8.320	0.015	0.015	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.025	0.002	12.463	0.037	0.037	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.051	-0.057	14.618	-0.063	-0.063	0.000	0.000	0.000	0.000
111	A	111	GLY	0	-0.004	0.012	17.831	-0.045	-0.045	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.095	-0.035	19.495	-0.059	-0.059	0.000	0.000	0.000	0.000
113	A	113	HIS	0	0.023	-0.005	20.834	0.026	0.026	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.016	0.005	21.978	-0.024	-0.024	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.858	-0.930	21.346	0.290	0.290	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.000	0.001	18.661	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.011	-0.012	21.827	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.883	-0.952	24.713	0.165	0.165	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.007	0.015	24.500	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	120	PHE	0	0.011	-0.002	27.288	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.046	-0.019	28.737	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.007	0.007	30.904	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.026	-0.069	32.199	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.035	0.011	29.381	0.011	0.011	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.876	-0.907	30.002	0.139	0.139	0.000	0.000	0.000	0.000
126	A	126	ILE	0	0.075	0.055	28.650	0.013	0.013	0.000	0.000	0.000	0.000
127	A	127	TYR	0	-0.005	-0.044	25.269	0.015	0.015	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.892	0.949	25.353	-0.121	-0.121	0.000	0.000	0.000	0.000
129	A	129	GLN	0	0.028	0.018	25.723	0.008	0.008	0.000	0.000	0.000	0.000
130	A	130	THR	0	0.018	0.018	21.968	0.019	0.019	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.785	0.877	21.275	-0.193	-0.193	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.859	-0.928	20.827	0.270	0.270	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.851	-0.910	20.921	0.323	0.323	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.026	-0.029	16.672	0.044	0.044	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.855	-0.929	16.788	0.399	0.399	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.954	-0.968	17.126	0.390	0.390	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.001	-0.006	15.699	0.044	0.044	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.018	-0.006	11.821	0.108	0.108	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.869	0.936	12.418	-0.311	-0.311	0.000	0.000	0.000	0.000
140	A	140	GLN	0	-0.033	-0.008	13.919	0.011	0.011	0.000	0.000	0.000	0.000
141	A	141	LEU	0	0.024	0.011	8.475	0.025	0.025	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.017	0.018	9.035	0.236	0.236	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.960	0.954	9.742	-0.472	-0.472	0.000	0.000	0.000	0.000
144	A	144	GLN	0	-0.073	-0.049	10.796	0.026	0.026	0.000	0.000	0.000	0.000
145	A	145	LEU	0	0.082	0.038	4.686	-0.197	-0.121	-0.001	-0.006	-0.069	0.000
146	A	146	LYS	1	0.920	0.980	6.929	-0.654	-0.654	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.816	0.915	9.150	-0.872	-0.872	0.000	0.000	0.000	0.000
148	A	148	ASP	-1	-0.824	-0.889	5.782	2.220	2.220	0.000	0.000	0.000	0.000
149	A	149	ARG	1	0.960	0.956	6.395	-0.132	-0.132	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.913	0.949	2.705	-3.119	-2.428	0.109	-0.197	-0.603	0.000
151	A	151	LEU	0	-0.080	-0.021	2.436	-5.936	-3.182	1.443	-1.609	-2.588	-0.011
152	A	152	GLU	-1	-0.949	-0.958	3.397	-0.743	0.323	0.204	-0.229	-1.040	-0.004

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)